Whole genome characteristics of coxsackievirus A6 in Hebei, 2011−2019

Objective  To analyze the whole genome characteristics and evolutionary recombination events of coxsackievirus A6 (CVA6) in Hebei province during 2011−2019.

Methods  The whole genome sequence of enterovirus was obtained by universal amplification of enterovirus genome. Enterovirus strains were isolated from mild and severe cases of hand, foot and mouth disease(HFMD) caused by CVA6. Sequence alignment and phylogenetic analysis were performed by using software MEGAX , gene recombination signals were detected by using software RDP4 , and gene recombination events were verified by using software package Sim Plots 3.5.1 .

Results The phylogenetic analysis indicated that the CVA6 isolates in Hebei mainly belonged to subtype D2 before 2012, and subtype D3 became predominant during 2013−2019. Whole genome sequencing obtained 13 complete sequences in two branches of 2C region and P3 region of the isolated subtype D3 strains.

Conclusion  Gene recombination occurred in CVA6 isolated in Hebei . It is necessary to update the whole genome sequence database of CVA6 to provide data support for the early warning of possible large-scale epidemic of HFMD caused byrecombinant enterovirus strains in this area.